Ligand profile

SPF

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_1025 — putative O-METHYLTRANSFERASE

Via homolog PDB 1sus UniProt Q40313 Formula C₃₂H₄₄N₇O₂₀P₃S
Mol. weight 971.72 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SPF
PDB
1sus
UniProt (similar protein)
Q40313
Target protein
VK055_1025

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 971.72 Da
LogP (Crippen) -0.15
H-bond donors 10
H-bond acceptors 22
TPSA 402.32 Ų
Rotatable bonds 21
Aromatic rings 3 / 5
Heavy atoms 63
Fraction sp³ C 0.50
Formula C₃₂H₄₄N₇O₂₀P₃S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 402.3
  • −1 ≤ LogP ≤ 5 -0.15
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 971.7
  • LogP ≤ 5 -0.15
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 22
Veber's rules Fail
  • Rotatable bonds ≤ 10 21
  • TPSA ≤ 140 Ų 402.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1([C@H](C1(C(=O)NCCC(=O)NCCSC(=O)\C=C\c2cc(c(c(c2)OC)O)OC)O)O[P@](=O)(O)O[P@](=O)(O)OC[C@@H]3[C@H]([C@@H]([C@@H](O3)n4cnc5c4ncnc5N)O)OP(=O)(O)O)C
InChI 
InChI=1S/C32H44N7O20P3S/c1-31(2)29(32(31,45)30(44)35-8-7-20(40)34-9-10-63-21(41)6-5-16-11-17(53-3)23(42)18(12-16)54-4)58-62(51,52)59-61(49,50)55-13-19-25(57-60(46,47)48)24(43)28(56-19)39-15-38-22-26(33)36-14-37-27(22)39/h5-6,11-12,14-15,19,24-25,28-29,42-43,45H,7-10,13H2,1-4H3,(H,34,40)(H,35,44)(H,49,50)(H,51,52)(H2,33,36,37)(H2,46,47,48)/b6-5+/t19-,24+,25-,28-,29-,32?/m1/s1
InChIKey 
HJGDVDUGXUSOGA-ADTMLPBESA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF01596

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_1025.

PDB 10

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 2

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)